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XRD1 Highlights

Every year, ELETTRA publishes 'ELETTRA Highlights' reporting a selection of the work done at the Laboratory during the last twelve months.
In this page you will find a brief presentation of the experiments done at the XRD1 beamline and present in ELETTRA Highlights, along with other relevant results obtained at the beamline.



2A7I_2
1WSW
1A9N
2VY0
3K9M
1FD9
3HJS
3H3U_2
1Z5R_2
2P1X
2A7I_2




C1–C4 alcohol–cavitand complexes

Crystal structures of two of the six cavitand-alcohol complexes. Geometric parameters describing the host-guest interaction, such as the H bond
length (Oalc⋅⋅⋅O=P) and distances of the hydroxyl and methyl groups from the mean plane of O atoms of P=O groups are reported in the top and
in the side views, respectively.















The crucial parameter to define the success of a given sensor is therefore selectivity, and for this reason the strategy to prepare the sensing material following the principle of supramolecular chemistry has quickly gained increasing importance. Here a new solid-state fluorescent sensor based on phosphonate cavitand for detecting short-chain alcohols in the gas phasehas been investigated.

Retrieve Article


Highly selective chemical vapor sensing by molecular recognition: specific detection of C1-C4 alcohols with a fluorescent phosphonate cavitand.

F. Maffei, P. Betti, D. Genovese, M. Montalti, L. Prodi, R. De Zorzi, S. Geremia, and E. Dalcanale, Angew. Chem. Int. Ed. 50, 4654 (2011) 10.1002/anie.201100738





Cuprate Superconductor



The disposition of defects in metal oxides is a key attribute exploited for applications from fuel cells and catalysts to superconducting devices and memristors.

This study reports the X-ray writing of high-quality superconducting regions, derived from defect ordering, in the superoxygenated layered cuprate, La2CuO4+y. Irradiation of a poor superconductor prepared by rapid thermal quenching results first in the growth of ordered regions, with an enhancement of superconductivity becoming visible only after a waiting time, as is characteristic of other systems such as ferroelectrics, where strain must be accommodated for order to become extended.

Retrieve Article


Evolution and control of oxygen order in a cuprate superconductor;
Nicola Poccia, Michela Fratini, Alessandro Ricci, Gaetano Campi, Luisa Barba, Alessandra Vittorini-Orgeas, Ginestra Bianconi, Gabriel Aeppli, Antonio Bianconi; Nature Materials (2011) 10.1038/nmat3088


Jack Bean Urease


ponn.pngFolding of the 10-kDa entomotoxic peptide region of JBU (Left) and the corresponding region in B. pasteurii bacterial urease (Right). The insecticidal region in bacterial urease is not intact and consists of two chains.

The three dimensional structure of the historic enzyme, the Jack bean urease (JBU) has recently been unraveled. JBU was not only the first enzyme isolated as a crystalline protein by Sumner in 1926, which fetched him the Nobel Prize, but also the first example of a nickel metalloenzyme and the first protein which showed the presence of sulfhydryl groups. Surprisingly, JBU had to wait more than 80 years for its structural revelation Retrieve Article


Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure; A. Balasubramanian and K. Ponnuraj, J.; Mol. Biol. 400, 274 (2010); 10.1016/j.jmb.2010.05.009


XRD1 Sample Changer

A new Sample Changer (SC) is available on the XRD1 as a result of an in-house development project at ELETTRA.

The SC has been designed to handle only SPINE standard sample holders and vials stored into cryo-vial baskets [Fig.1], following the standard already established at ESRF beamlines (SC3 system as sample changer). 5 baskets (i.e. up to 50 samples) can be loaded into the dispensing dewar of the SC where they lie in a liquid nitrogen bath.
The control of the instrumentation is performed through a GUI (called ‘Sample Changer Control’), which can be opened from the main Beamline Control Panel, both inside and outside the experimental hutch of the beamline [Fig.2].

Basket Loading

The first step deals with the loading of the cryo-vial baskets. Each basket must be inserted into (and later removed from) the loading aperture of the dispensing dewar by means of the proper transfer tool available at the experimental table. The loading aperture is made available by removing the plug with the handle; this of course must be repositioned once the loading/unloading procedure is terminated. Once catched the basket with the transfer tool, the angular positioning groove of the basket must be oriented as indicated by the arrow on the box of the SC in order to properly insert the basket into the basket holder [Fig. 3].

There are 5 different basket holders in the inner carousel, so the loaded baskets are labeled from 1 to 5 in order to distinguish them. The loading procedure can be managed by means of a button panel available at the experimental table:

  1. Button 1 initializes the procedure and moves the basket holder #5 at the loading position, ready to accept the first basket.
  2. Pressing Button 2, the following basket holder (which is #4, then #3 and so on) reaches the loading position: the mounting natural sequence is 5,4,3,2,1.
  3. Once loaded all the baskets (up to 5) and closed the loading aperture, the user can exit the hutch and start the experiment.

During the procedure the GUI shows the basket position and can also be used instead of the button panel to select the desired basket to be loaded/unloaded/changed.

Sample Decoding

One can rely on a DataMatrix decoding procedure in order to use the datamatrix code of the sample holders (see SPINE standard) to identify the samples. Once loaded the baskets the user can start through the GUI the “Scan All Baskets” procedure, which takes about 15 minutes to try to decode each sample of each basket. Also “Scan selected basket” procedure can be launched, for example when only one basket has been inserted or changed.
This facility is very helpful for users who want to safely track a big amount of crystals: they can import their own comments on their samples identified by the datamatrix codes by means of properly built csv files. The GUI provides an additional comment column for final remarks after X-rays exposition.

Sample Mounting

Decoding procedure is available but not mandatory, of course. Once loaded the baskets the samples are ready to be safely mounted (and then dismounted) by the SC: the user selects the desired sample and press the ‘Pick up’ button to get it transferred on the goniometer head in vertical position; this ‘Top’ geometry assures the wet transfer of the samples to (and from) the measurement position, where they are cooled by a Oxford crycooler. At this point the usual centering procedure (2-click centering on the ‘Crystal Centering’ window) can be used to center the sample on the beam trajectory, in order to prepare the crystal exposition. After the exposure (be it one shot to check the crystal quality or any data collection set) the user can remove the sample by pressing the ‘Remove’ button, getting ready for the mounting of some other sample.

figure1.jpg
Fig.1. Top-left. SPINE standard for sample holders and vials: it also imposes a fixed length of 22 mm for the whole sample holder (18 mm for the pin) and presents a 10 character identification code. SPINE sample holders and vials can be obtained from Molecular Dimensions Limited (MDL). Vials from Hampton Research (HR) are not fully supported at the present, but are usable. Bottom. Datamatrix codes on the base of the caps; on the left two caps from MDL, on the right one from HR: according to our experience MDL caps may become rusty by use as shown, so we recommend to pay attention to the conditions of your sample holders or use HR model, if you want to rely on the possibility to perform Datamatrix recognition. Top-right. Cryo-vial baskets can be obtained from crystallographic kits of MDL: each can store 10 cryo-vials. One can distinguish also the groove which is used determine the angular positioning.

gui_frames.jpg

Fig.2. The Graphical User Interface. On the right frame, the possibility to load/unload and scan for decoding a selected basket (as well as all baskets): the list shows the result of decoding for the 10 basket samples. In the central frame,  the possibility to mount (unmount) the selected sample on the measurement position.

loading.jpg

Fig.3. An overview of the top of the SC with the components involved in the loading basket procedure. The transfer tool (1) catching the cryo-basket to be inserted into the loading aperture (2). The arrow (3) indicates the position of the angular groove of the basket so to help it enter inside the basket holder in the SC. The aperture must be finally closed by remounting the plug (4).


Carbonic Anhydrase

pol.medium.png















Stereoview of the electron density map and corresponding models of HCAII active site in complex with (a) CO2 at 1.56 A resolution and (b) HCO3- at 1.66 A resolution. The bicarbonate has van der Walls contacts with the same residues as CO2.

Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid–base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131–137], but a structure of an HCAII in complex with CO2 or HCO3 has remained elusive.
Here, we report previously undescribed structures of

HCAII:CO2 and HCAII:HCO3 complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray.

Retieve Article


Structural study of X-ray induced activation of carbonic anhydrase; Sjöblom B., Polentarutti M. and Djinović-Carugo K., PNAS 106, 10609 (2009); doi:10.1073/pnas.0904184106



PDI8CN2 for n-Type Thin-Film Transistors



Schematic drawing of the crystal structure of PDI8CN2. 2D-GIXD experimental and simulated images. Copyright 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiscale investigation of N,N’-bis(n-octyl)-x:y, dicyanoperylene-3,4:9,10-bis(dicarboximide), PDI8CN2, n-type semiconductor, consisting in the characterization of the crystallographic structure and morphology of molecular films.GIXRD (Grazing Incidence X Ray Diffraction) and AFM (AtomicForce Microscopy) measurements reveal that the crystalline order and the growth mechanism of PDI8CN2 films depend on the deposition temperature.

We show how these features are highly correlated with the electrical response of PDI8-CN2-based

field-effect transistors.


Retieve Article


Structure and Morphology of PDI8-CN2 for n-Type Thin-Film Transistors; Liscio F., Milita S., Albonetti C., D’Angelo P., Guagliardi A., Masciocchi N., Della Valle R.G., Venuti E., Brillante A. and Biscarini F., Adv. Funct. Mater. 22, 943 (2012); doi: 10.1002/adfm.201101640



Crystal structures of human legumain unveil activation mechanisms to distinct peptidase activities



Structure and regulation of (pro-)legumain. Top-view on the AEP active site shows how Glu190 stabilizes the protonated state of Cys189 Sg.

The cysteine protease legumain is a key player in immunity and cancer at different cellular locations, some of which are incompatible with its pH-stability. We solved the crystal structures of zymogenic and active legumain, unveiling its activation and regulation principles. Legumain contains an Asn-specific endopeptidase activity that is electrostatically released at acidic pH. Surprisingly, we uncovered a complementary proteolytic activation route, generating a carboxypeptidase activity. The context-dependent activation of legumain reconciles its partly conflicting moonlighting activities.


Retieve Article


Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation; Dall E. and Brandstetter H., Proc Natl Acad Sci USA 110, 27 (2013); doi: 10.1073/pnas.1300686110





Structure of Human NAPE-PLD: Regulation of Bioactive Lipids Biosynthesis by Bile Acids


NAPE-PLD (N-acyl phosphatidylethanolamine phospholipase D) is a key membrane-bound enzyme involved in the biosynthesis of endocannabinoids and other bioactive lipid signaling amides.
Highly detailed structural findings, obtained on XRD1, provide the structural basisto understand how this protein is tightly connected to mammal’s neurotransmission and a variety of pathophysiological processes, including gastrointestinal motility, synaptic plasticity, appetite and mood.

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Structure of human NAPE-PLD: regulation of fatty-acid ethanolamide biosynthesis by bile acids; Magotti P, Bauer I, Igarashi M, Babagoli M, Marotta R, Piomelli D, Garau G, Structure 23, 3 (2015) doi:10.1016/j.str.2014.12.018






Customizing Properties of beta-Chitin in Squid Pen by Chemical Treatments


Natural bio-products and processes are becoming more and more important for the preparation of new materials.

The squid pen from the Loligo vulgaris was used for preparation of beta-chitin materials characterized by different chemical, micro- and nano-structural properties that preserved, almost completely the macrostructural and the mechanical ones. The potential applications of these beta-chitin materials range from nanotechnology to regenerative medicine. This kind of materials, which are waste products

of the fishing industry, has also important environmental implications.


Retieve Article


Customizing Properties of β-Chitin in Squid Pen (Gladius) by Chemical Treatments; Ianiro A, Giosia MD, Fermani S, Samorì C, Barbalinardo M, Valle F, Pellegrini G, Biscarini F, Zerbetto F, Calvaresi M, Falini G., Marine Drugs. 2014; 12(12):5979-5992 doi:10.3390/md12125979




Expression-Enhanced Fluorescent Proteins Based on Enhanced Green Fluorescent Protein for Super-resolution Microscopy


The first ever crystal structures of a negative reversibly switchable fluorescent protein derived from Aequorea victoria - called rsGreen0.7 -was determined in both the “on”- and “off”-conformation and provided further insights into the mechanisms underlying the photochromism. During photoswitching several structural rearrangements such as a cis-trans isomerization, backbone shifts and changes in hydrogen bonding occur.

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Expression-Enhanced Fluorescent Proteins Based on Enhanced Green Fluorescent Protein for Super-resolution Microscopy; Duwé S., De Zitter E., Gielen V., Moeyaert B., Vandenberg W., Grotjohann T., Clays K.,
Jakobs S., Van Meervelt L., and Dedecker P., ACS NANO, Article ASAP (2015) 10.1021/acsnano.5b04129




Multitarget drug design strategy: tacrine-quinone hybrids designed to block amyloid-ß aggregation and to exert anticholinesterase and antioxidant effects

Multitarget anti-Alzheimer compounds 1-3, designed by combining a naphthoquinone function and a tacrine fragment, displayed excellent in vitro AChE (AcetylCholinEsterase) inhibitory potencies and proved to be effective as Aß (Amyloidß) anti-aggregants. The x ray analysis of 2 in complex with AChE allowed rationalizing the outstanding activity data, IC50 = 0.72nM.
The non toxic derivatives 2 and 3: (i) completely reverted the decrease in viability induced by Aß in immortalized cortical neurons; (ii) showed antioxidant activity in human glioma; and (iii) crossed the blood-brain barrier.

Retrieve Article


Multitarget Drug Design Strategy: Quinone–Tacrine Hybrids Designed To Block Amyloid-β Aggregation and To Exert Anticholinesterase and Antioxidant Effects, Nepovimova E, Uliassi E, Korabecny J, Peña-Altamira LE, Samez S, Pesaresi A, Garcia GE, Bartolini M, Andrisano V, Bergamini C, Fato R, Lamba D, Roberti M, Kuca K, Monti B, Bolognesi ML
J. Med. Chem., Vol. 57 - 20, pp. 8576-8589 (2014); doi: 10.1021/jm5010804



Single-Crystal Structure Determination of Hydrogen-bonded Organic Pigments

Hydrogen-bonded pigments are a class of industrial colorants that have recently emerged as highly promising electronic materials. Elucidating the crystalline structure of these materials is crucial to understand the mechanisms of charge transport and optimizing them for electronics. High-resolution X-ray diffraction using Elettra synchrotron radiation has allowed the unraveling of a crystal structure that has remained mysterious for decades, and has also been used to characterize novel hydrogen-bonded pigments. Retrieve article


Epindolidiones—Versatile and Stable Hydrogen-Bonded Pigments for Organic Field-Effect Transistors and Light-Emitting Diodes, Glowacki ED, Romanazzi G, Yumusak C, Coskun H, Monkowius U, Voss G, Burian M, Lechner RT, Demitri N, Redhammer GJ, Sünger N, Suranna GP, Sariciftci S
Advanced Functional Materials, Vol. 25 - 5, pp. 776-787 (2015); doi: 10.1002/adfm.201402539




Pore flexibility underlies the poor selectivity of CNG channels: a structural, functional and computational analysis



Cyclic nucleotide-gated (CNG) channels play important roles in transmitting information about vision and smell from sensory cells to the

brain, and share a high degree of similarity with K+ channels. Whereas K+ channels discriminate with high accuracy Na+ from K+, CNG channels do not discriminate among different cations. By combining electrophysiology, molecular dynamics simulations and X-ray crystallography we found that the pore region exhibits a dynamic structure and the pore diameter critically depends on the ion within.

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A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels, Napolitano LMR, Bisha I, De March M, Marchesi A, Arcangeletti M, Demitri N, Mazzolini M, Rodriguez A, Magistrato A, Onesti S, Laio A, Torre V
Proceedings of the National Academy of Sciences, Vol. 112 - 27, pp. E3619-E3628 (2015), doi: 10.1073/pnas.1503334112



Extended O-Doped Polycyclic Aromatic Hydrocarbons


a) SEM images of polyaromatic molecular crystals displaying a lamellar-like texture; b) solid-state columnar π-π stacks with an interplanar distance of 3.3Å



The synthesis of O-doped benzorylenes, in which peripheral carbon atoms have been replaced by oxygen atoms, has been achieved for the first time. This includes key high-yielding ring-closure steps which, through intramolecular C-O bond formation, allow stepwise planarization of oligonaphthalenes. Single-crystal X-ray diffraction showed that the tetraoxa derivative forms remarkable face-to-face π–π stacks in the solid state, a favorable solid-state arrangement for organic electronics.


Retrieve Article


Extended O-Doped Polycyclic Aromatic Hydrocarbons; Stassen D., Demitri N., Bonifazi D.,

Angew. Chem. 2016, 128, 1 – 6
doi: 10.1002/ange.201509517








Cisplatin Encapsulation within the Ferritin Nanocage: A High-Resolution Crystallographic Study


CDDP-encapsulated AFt appears to be an ideal nanocarrier for CDDP delivery to target sites, as it possesses a high biocompatibility and can be internalized by receptor mediated endocytosis thus carrying the drug to tumor tissue with higher selectivity than free CDDP.
N Pontillo et al., Chem. Commun., 2016

Cisplatin (CDDP) can be encapsulated within the central cavity of reconstituted (apo)ferritin, (A)Ft, to form a drug-loaded protein of potential great interest for targeted cancer treatments. In this study, the interactions occurring between cisplatin and native horse spleen Ft in CDDP-encapsulated AFt  are  investigated  by  high-resolution  X-ray crystallography. A protein bound Pt center is unambiguously identified in AFt subunits by comparative analysis of difference Fourier electron density maps and of anomalous dispersion data. Indeed, a [Pt(NH3)2 H2O]2+ fragment is found coordinated to the His132 residues located onthe inner surface of the large AFt spherical cage.

Remarkably, Pt binding does not alter the overall physicochemical features (shape, volume, polarity/hydrophobicity and electrostatic potential) of AFt nanocage outer surface.


Retrieve Article

Cisplatin Encapsulation within the Ferritin Nanocage: A High-Resolution Crystallographic Study;
N Pontillo, F Pane, L Messori, A Amoresano, and A Merlino,

Chem. Commun., 2016;
doi:10.1039/C5CC10365G








Crystal structure of the earthworm toxin reveals the mechanism of assembly and its potential application



Crystal structure of the lysenin pore, PDB-ID 5EC5, shown in ribbons, top view. Each of the nine protomoeric units is presented in a different color.
Podobnik M. et al., Nature Communications, 7:11598 (2016)



Pore forming compounds are almost exclusively toxic peptides or proteins, which are expressed by the producing organism as water-soluble monomers, attracted by the membranes via specific receptors. The most studied pore-forming proteins are various families of bacterial toxins, termed pore-forming toxins (PFTs). Bacterial PFT serve as important virulence factors promoting bacterial spread through invading cells and tissues. However, PFTs are not limited to bacteria, and are found in many other organisms.
In this study we have determined the three dimensional atomic structure of the toxin from the earthworm Eisenia fetida, called lysenin. Lysenin is present in the coelomic fluid of earthworms and is produced to act defensively against parasitic microorganisms by forming pores.  The toxin is excreted by the defending cells, which are part of the immune system of the earthworm. It then

binds to cellular membranes and forms pores in them. Such damage usually leads to the death of the target cell
 

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Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly;
Podobnik M., Savory P., Rojko N., Kisovec M., Wood N., Hambley R., Pugh J., J. Wallace E., McNeill L., Bruce M., Liko I., Allison T. M., Mehmood S., Yilmaz N., Kobayashi T., Gilbert R. J. C., Robinson C. V., Jayasinghe L. and Anderluh G.
Nature Communications, 7:11598 (2016),
DOI: 10.1038/ncomms11598





Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ³-oxo)Tris[(μ²-peroxo)] triiron(III) cluster



After 60 min exposure to a ferrous solution, a fully assembled (μ3-oxo)Tris[(μ2-peroxo)(μ2-glutamato-κO:κO′)](glutamato-κO)(diaquo)triiron(III) anionic cluster appears in human L-ferritin.

Pozzi C. et al., Proceedings of the National Academy of Sciences 2017


Iron is an essential element in biology but has limited bioavailability. Ferritins are 24-mer iron-storage nanocage proteins that concentrate iron in their inner compartment as a bioavailable iron oxide biomineral. In L-type subunits, abundant in ferritins from organs involved in long-term iron storage, the biomineralization has been proposed to proceed through nucleation events involving iron(II) oxidation at the inner cage surface. Here, authors demonstrate the nature and structural features of these nucleation sites. Structures captured during iron uptake show that the formation of the iron biomineral proceeds via the assembly of a tri-nuclear iron cluster, anchored to the protein through glutamic acid side chains,

and involving oxo and peroxo ligands that are produced during the iron(II) oxidation by dioxygen.

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Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ3-oxo)Tris[(μ2-peroxo)] triiron(III) cluster; Pozzi C., Ciambellotti S., Bernacchioni C., Di Pisa F., Mangani S., and Turano P.
Proceedings of the National Academy of Sciences 2017
doi: 10.1073/pnas.1614302114







Layered metal-functionalized covalent organic frameworks as precursors of supercapacitive porous N-doped graphene

Scheme of the work showing the COF-1 structure, the metal coordination COF-1-M and the calcination process to produce N-doped graphenes. This strategy avoids the need of the use of any additional template, allowing the formation of corrugated graphene in a one-pot reaction from the COF-1–M precursors.

J. Romero. et al., J. Mater. Chem. A, 5, 4343, (2017)



A crystalline and porous layered covalent organic framework (COF) based on polyimine has shown the ability to link FeIII, CoII and NiII into its cavities. The structure and morphology of these functionalized COFs enable to generate N-doped porous graphene upon controlled calcination. The so formed highly corrugated and N-doped porous graphene sheets exhibit high values of specific capacitance that make them useful as electrode material for supercapacitors.

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Metal-functionalized covalent organic frameworks as precursors of supercapacitive porous N-doped graphene ;
Romero J, Rodriguez-San-Miguel D, Ribera A, Mas-Ballesté R, Otero TF , Manet I, Liscio F, Abellán G, Zamora F, Coronado E,
J. Mater. Chem. A, 5, 4343, (2017); DOI: 10.1039/c6ta09296a








The mechanism of sliding of the human DNA clamp PCNA

X-ray crystallography: the 2.8 Å crystal structure of the human PCNA homotrimer bound to a 10 bp DNA duplex. A close-up shows the detailed interactions between the DNA phosphates (yellow spheres) and a set of positively charged residues within the PCNA central channel.

De March, M. et al., Nat.Commun. 8, 13935 (2017)


DNA sliding clamps are ring-shaped proteins that encircle the DNA and harbour the polymerases, the enzymes that replicate DNA, allowing the duplication of the genetic material. How DNA clamps move onto the DNA double helix has remained elusive due to the peculiar nature of the interaction between the clamp and DNA. By a combination of x-ray crystallography, nuclear magnetic resonance (NMR), and molecular dynamics (MD) data, we have elucidated the molecular mechanism of sliding of the human clamp PCNA on DNA, a spiral motion that keeps the orientation of PCNA competent for binding to the replicative polymerase.

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A structural and computational analysis reveals the mechanism of sliding of the human DNA clamp PCNA, a central player in DNA replication;
De March M, Merino N, Barrera-Vilarmau S, Crehuet R, Onesti S, Blanco FJ, De Biasio A,
Nat.Commun. 8, 13935 (2017); doi: 10.1038/ncomms13935




How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin

The positions of bound xenon and krypton in the crystal structure can be unambiguously identified in the electron density due to their anomalous scattering properties. Both types of noble gases populate the same position in the S1′ cavity.

Krimmer S G et al., J. Am. Chem. Soc., 2017, 139 (30), pp 10419–10431
The hydration state of deep, well-accessible hydrophobic pocket of the metalloprotease thermolysin has been investigated using high-resolution crystallography and isothermal titration calorimetry to understand solvent effects in protein−ligand interactions, a key topic in drug design. The enzyme accessibility could be proved by accommodating noble gas atoms into the pocket in the crystalline state. The noble gases xenon and krypton are known to preferentially bind to desolvated, hydrophobic protein cavities through weak van der Waals interactions. These atoms can, therefore, be used as experimental probes to detect such cavities.

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How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin.

Krimmer S G, Cramer J, Schiebel J, Heine A, Klebe G, J. Am. Chem. Soc., 2017, 139 (30), pp 10419–10431 DOI: 10.1021/jacs.7b05028





Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins

The picture presents the structural change in NLP protein upon sugar binding: crystal structures of NLP before (blue, left) and after glucosamine binding (green, right) on the background.

Lenarčič T et al. , Science, 2017, 358, pp 1431-1434
Van den Ackerveken G, Science, 2017, 358, Issue 6369, pp. 1383-1384


NLP proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. NLP refers to “Necrosis and ethylene-inducing peptide 1–like proteins”, describing effects of these proteins in target plants, i.e. tissue cell death (necrosis) and production of the plant hormone ethylene, produced in response to environmental stress. Many NLPs are cytotoxins that facilitate microbial infection of eudicot plants (like tomato and tobacco), but not of monocots (like cereals and leek). The molecular basis of such specificity of members of the NLP family of toxins has been revealed through data collected on XRD1 beamline.
Further informations can be found at: http://www.elettra.eu/science/top-stories/an-extra-sugar-provides-protection.html

Retrieve Article

Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins,
Lenarčič T, Albert I, Böhm H, Hodnik V, Pirc K, Zavec A B, Podobnik M, Pahovnik D, Žagar E, Pruitt R, Greimel P, Yamaji-Hasegawa A, Kobayashi T, Zienkiewicz A, Gömann J, Mortimer J C, Fang L, Mamode-Cassim A, Deleu M, Lins L, Oecking C, Feussner I, Mongrand S, Anderluh G, Nürnberger T
Science, 2017, 358, pp 1431-1434
DOI 10.1126/science.aar4188

How plants differ in toxin-sensitivity, Van den Ackerveken G, Science, 2017, 358, Issue 6369, pp. 1383-1384
DOI: 10.1126/science.aar4188


 



Single-point mutation, metal ion concentration and low dielectric constant of the medium induce human ubiquitin aggregation



Ribbon representation of the asymmetric unit content (chains A,B and C) plus one symmetriy-related molecule of chain B (B*), of E16V crystal grown at 35 mM Zn2+. The metal sites (ZN1, Zn5, Zn6 and Zn7) are represented as yellow spheres. The side chain of the mutated residue (Val16) is shown as red sticks

Fermani S et al, Chem. Eur. J., 2017, 24, pp 4140

Human ubiquitin (hUb) is a small and stable globular protein involved in several aspects of cell physiology. Interest in aggregation pathways of human ubiquitin (hUb) stems from hUb-positive aggregates being biomarkers of neurodegenerative diseases. Two hUb dimers have been recognized as possible precursors of amyloid-like aggregates, but their formation is disfavored by electrostatic repulsions involving mainly Glu16. Substitution of Glu16 negative charge by a metal ion and a decrease of the dielectric constant of the medium can also induce hUb aggregation
Retrieve Article

Aggregation Pathways of Native‐Like Ubiquitin Promoted by Single‐Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium;
Fermani S, Calvaresi M, Mangini V, Falini G, Bottoni A, Natile G, Arnesano F, Chem. Eur. J., 2018, 24, pp 4140
DOI: 10.1002/chem.201705543


Photosynthesis – The dark side structural proteome is now completed



The crystal structure of the phosphoribulokinase (PRK) – the last enzyme of the Calvin-Benson cycle – has been finally solved, completing its redox structural proteome. The PRK structure also allowed to shed light on the molecular evolution of PRKs in eukaryotes.
Gurrieri L. et al. , Proceedings of the National Academy of Sciences Mar 2019, 201820639

The Calvin-Benson cycle is the set of chemical reactions that take place in chloroplasts during photosynthesis.  The cycle is light-independent (dark) because it takes place after the energy has been captured from sunlight. It consists of 13 distinct reactions catalysed by 11 enzymes. Among these, the phosphoribulokinase (PRK) had notably still to be characterized at the atomic scale. To accomplish this goal and complete the redox structural proteome of the CB cycle, authors determined the crystal structures of PRK from two model species: the green alga Chlamydomonas reinhardtii (CrPRK) and the land plant Arabidopsis thaliana (AtPRK). Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both AtPRK and CrPRK have a strongly reduced dimer interface and an increased

number of random coiled regions, suggesting a general loss in structural rigidity during molecular evolution of PRKs in eukaryotes.

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Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin–Bensoncycle;
Gurrieri L., Del Giudice A., Demitri N., Falini G., Viorel Pavel N., Zaffagnini M., Polentarutti M.,  Crozet P., Marchand C. H., Henri J., Trost P., Lemaire S. D., Sparla F., Fermani S.
Proceedings of the National Academy of Sciences Mar 2019, 201820639; DOI: 10.1073/pnas.1820639116

 


Nanoparticles – New light on growth mechanisms



Synchrotron X-Ray diffraction in solution is used to shed light on the growth mechanisms of the coprecipitation of iron oxide nanoparticles, showing an initial precipitation of iron hydroxide carbonate [Fe6(OH)12CO3] and ferrihydrite and the successive growth of ferrihydrite /via/ the re-dissolution of iron hydroxide carbonate to form a final magnetite phase.
LaGrow A P et al., Nanoscale, 2019,11, 6620-6628

Iron oxide nanoparticles are used extensively in applications in biomedicine, magnetic storage media, water treatment and catalysis. The most ubiquitous synthetic method to date is the co-precipitation method, which is carried out in aqueous solutions containing ferric (Fe3+) and ferrous (Fe2+) salts as precursors, to which a base is added at moderate temperatures (<100 °C).
Even though the co-precipitation reaction is widely used, the mechanism of the reaction is still poorly understood, due to a severe lack of information on how intermediates are formed.
Synchrotron X-ray diffraction revealed the initial formation of crystalline iron hydroxide carbonate (green rust) plates occurringbefore the Fe3O4/γ-Fe2O3 appeared. The ferrihydrite particles increase in size over time as the proportion of iron hydroxide carbonate plates are re-dissolved into solution, until the ferrihydrite particles crystallise into Fe3O4/γ-Fe2O3.
A new particle formation mechanism is detailed,

differing drastically from the most commonly discussed classical nucleation and growth process. Such comprehensive understanding of the mechanism is essential not only for robust syntheses, but also for the tuning of particle properties for the targeted applications. In particular, the growth mechanism shows a separation of the nucleation and growth stages in the reaction which will allow chemists greater control over the size of the nanoparticles that can be readily synthesised via co-precipitation.

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Unravelling the growth mechanism of the coprecipitation of iron oxide nanoparticles with the aid of synchrotron X-Ray diffraction in solution; LaGrow A P, Besenhard M O, Hodzic A, Sergides A, Bogart L K, Gavriilidis A,Thanh N T K,
Nanoscale, 2019,11, 6620-6628; 
DOI: 10.1039/C9NR00531E

 

 

Ultima modifica il Lunedì, 15 Luglio 2019 13:50